With the advent of whole slide digital scanners, histological data has become amenable to digital and quantitative image analysis, as discussed in Madabhushi, A., Digital pathology image analysis: opportunities and challenges, Imaging in Medicine, 1:7-10, (2009) and Alexe, G. et al., Towards improved cancer diagnosis and prognosis using analysis of gene expression data and computer aided imaging, Experimental Biology and Medicine, 234:860-879 (2009), the disclosures of each of which are hereby incorporated by reference. Additionally, with tissue microarray (“TMA”) technology it is possible to simultaneously stain several hundred sections (tissue cylinders) for the presence of various biomarkers. In the digital uncompressed form, these TMA's can be several gigabytes in size with image dimensions of 100,000×100,000 pixels. Some researchers currently are looking to increase the size of cylinders that can be accommodated on a single TMA to over 10,000, as discussed in Rui, H., et al., Creating tissue microarrays by cutting-edge matrix assembly, Expert Rev. Med. Devices, 2(6):673-680 (2005), the disclosure of which is hereby incorporated by reference. Human visual analysis of such large amounts of data is not easily done, requires a highly trained observer, and is also subject to many reasons for inaccurate and/or inconsistent analysis. Therefore, high-throughput, reproducible and accurate computerized image analysis methods are required for quantification of the presence and extent of different biomarkers within TMAs. The present disclosure describes such a system that overcomes these shortcomings of existing analysis techniques.